The influence of viral and bacterial community diversity on pathogenic E. coli prevalence in pre-harvest cattle

Department: University of Delaware, Department of Plant and Soil Sciences

Publisher: University of Delaware

Date Issued: 2015

Abstract: Since 1982, Shiga toxin-producing Escherichia coli (STEC) has been an infamous foodborne pathogen causing significant human illness worldwide. The past decades have brought much advancement in food safety practices and industry standards, but STEC still remains prevalent in beef processing with cattle hide implicated as a major source of carcass contamination. To investigate the association between STEC prevalence and the indigenous microbial population of the hide, 16S rRNA bacterial community profiles and viral shotgun metagenomes were created from hide and fecal samples collected from a large commercial feedlot. For the 16S rRNA dataset, fecal OTUs were subtracted from the OTUs found within each hide 16S amplicon library to focus on bacterial populations found exclusively on the hide. Comparative alpha diversity analysis revealed a significant correlation between low bacterial diversity and samples positive for the presence of E. coli O157:H7 and/or the non-O157 groups. This trend continued regardless of diversity metric or fecal OTU presence. Beta diversity data revealed differences in the bacterial community composition between the O157 and non-O157 contamination states, with certain OTUs demonstrating significant changes in relative abundance. The exact nature of this relationship remains a mystery, however phage interaction may play a crucial role due to their ability to control the diversity, abundance and genetic composition of their microbial host populations. By dissecting the population ecology of viral groups present in the fecal viral metagenomes we were able to uncover trends in phage host interactions between the feces and the hide and associations between virulent phage and the commensal microbes.